{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "819e8193",
   "metadata": {},
   "outputs": [],
   "source": [
    "# For now, we still need to manually add atomworks dependency\n",
    "import sys;\n",
    "sys.path.insert(0, '/home/jbutch/Projects/HT25/af3/rfd3-release/lib/atomworks/src')\n",
    "sys.path.append('/home/jbutch/Projects/HT25/af3/rfd3-release/models/rfd3/src')\n",
    "sys.path.append('/home/jbutch/Projects/HT25/af3/rfd3-release/src')\n",
    "\n",
    "from atomworks.io.utils.visualize import view"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d944272a",
   "metadata": {},
   "source": [
    "# 1) Design with RFD3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "137dbccd",
   "metadata": {},
   "outputs": [],
   "source": [
    "from rfd3.engine import RFD3InferenceConfig, RFD3InferenceEngine\n",
    "from rfd3.inference.input_parsing import DesignInputSpecification\n",
    "conf = RFD3InferenceConfig(\n",
    "    ckpt_path='/projects/ml/aa_design/models/rfd3_latest_cleaned.ckpt',\n",
    "    diffusion_batch_size=2,\n",
    "    dump_trajectories=True,\n",
    "    inference_sampler={\"num_timesteps\": 10},\n",
    ")\n",
    "# Lazily initialize model\n",
    "model = RFD3InferenceEngine(**conf)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2d422b11",
   "metadata": {},
   "outputs": [],
   "source": [
    "spec = DesignInputSpecification(\n",
    "    input='/home/jbutch/Projects/HT25/af3/rfd3-release/models/rfd3/tests/test_data/amidase_LOW.pdb',\n",
    "    length=10,\n",
    "    ligand='L:G',\n",
    "    unindex='A92-96,B2,E5',\n",
    "    select_fixed_atoms={\n",
    "        'B2': 'ND1,CG,NE2,CD2,CB,CE1',\n",
    "        'E5': \"OH,CZ,CE1,CE2,CD2,CD1,CG,CB\"\n",
    "    }\n",
    ")\n",
    "view(spec.build())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "050d7613",
   "metadata": {},
   "outputs": [],
   "source": [
    "outputs = model.run(\n",
    "    inputs=spec,\n",
    "    n_batches=1,\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "de18ec69",
   "metadata": {},
   "outputs": [],
   "source": [
    "for idx, data in outputs.items():\n",
    "    print(f\"Output type for batch {idx}: {type(data)}[0] = {type(data[0])}\")\n",
    "    print(f\"Output atom_array: {data[0].atom_array}\")\n",
    "    atom_array = data[0].atom_array\n",
    "view(atom_array)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d07ae413",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "rfd3-release",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.12.3"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}
